Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/WrappPlotCoverage.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from optparse import OptionParser
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3 import tarfile
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 import re
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 import shutil
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 import subprocess
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8
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9 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
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10
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 def toTar(tarFileName, directory):
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12 fileName = os.path.splitext(tarFileName)[0]
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13 fileNameBaseName = os.path.basename(fileName)
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14 tfile = tarfile.open(fileName + ".tmp.tar", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 list = os.listdir(directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 for file in list:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 if re.search(str(fileNameBaseName), file):
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18 tfile.add(file)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 tfile.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 if __name__ == "__main__":
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25
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26 # parse command line
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27 description = "Plot Coverage v1.0.1: Plot the coverage of the first data with respect to the second one. [Category: Visualization]"
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28
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 parser = OptionParser(description = description)
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30 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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31 parser.add_option("-f", "--inputFormat1", dest="inputFormat1", action="store", type="string", help="format of input file 1 [compulsory] [format: transcript file format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 parser.add_option("-g", "--inputFormat2", dest="inputFormat2", action="store", type="string", help="format of input file 2 [compulsory] [format: transcript file format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 parser.add_option("-q", "--sequence", dest="inputSequence", action="store", default=None, type="string", help="input sequence file [format: file in FASTA format] [default: None]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 parser.add_option("-o", "--output", dest="outTarFileName", action="store", type="string", help="output file [compulsory] [format: output file in zip format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 parser.add_option("-w", "--width", dest="width", action="store", default=1500, type="int", help="width of the plots (in px) [format: int] [default: 1500]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 parser.add_option("-e", "--height", dest="height", action="store", default=1000, type="int", help="height of the plots (in px) [format: int] [default: 1000]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 parser.add_option("-t", "--title", dest="title", action="store", default="", type="string", help="title of the plots [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 parser.add_option("-x", "--xlab", dest="xLabel", action="store", default="", type="string", help="label on the x-axis [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 parser.add_option("-y", "--ylab", dest="yLabel", action="store", default="", type="string", help="label on the y-axis [format: string]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 parser.add_option("-p", "--plusColor", dest="plusColor", action="store", default="red", type="string", help="color for the elements on the plus strand [format: string] [default: red]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 parser.add_option("-m", "--minusColor", dest="minusColor", action="store", default="blue", type="string", help="color for the elements on the minus strand [format: string] [default: blue]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 parser.add_option("-s", "--sumColor", dest="sumColor", action="store", default="black", type="string", help="color for 2 strands coverage line [format: string] [default: black]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 parser.add_option("-l", "--lineColor", dest="lineColor", action="store", default="black", type="string", help="color for the lines [format: string] [default: black]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 parser.add_option("-1", "--merge", dest="merge", action="store_true", default=False, help="merge the 2 plots in 1 [format: boolean] [default: false]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 (options, args) = parser.parse_args()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48
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49 absPath = os.getcwd()
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50 directory = "/tmp/wrappPlotCov"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 if not os.path.exists(directory):
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52 os.makedirs(directory)
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53 os.chdir(directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 if options.inputFileName1 != None and options.inputFormat1 != None and options.inputFileName2 != None and options.inputFormat2 != None and options.outTarFileName != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 print 'outputfile is :', outputFileName
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57 cmd = "python %s/Java/Python/plotCoverage.py -i %s -f %s -j %s -g %s -o %s -D %s" % (SMART_PATH, options.inputFileName1, options.inputFormat1, options.inputFileName2, options.inputFormat2, outputFileName, directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 if options.inputSequence!= None:
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59 cmd += " -q %s" % options.inputSequence
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 if options.width != None:
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61 cmd += " -w %s" % options.width
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62 if options.height != None:
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63 cmd += " -e %s" % options.height
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64 if options.title != None:
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65 cmd += " -t %s" % options.title
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66 if options.xLabel != None:
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67 cmd += " -x %s" % options.xLabel
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68 if options.yLabel != None:
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69 cmd += " -y %s" % options.yLabel
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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70 if options.plusColor != None:
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71 cmd += " -p %s" % options.plusColor
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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72 if options.minusColor != None:
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73 cmd += " -m %s" % options.minusColor
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74 if options.sumColor != None:
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75 cmd += " -s %s" % options.sumColor
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76 if options.lineColor != None:
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77 cmd += " -l %s" % options.lineColor
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78 if options.merge:
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79 cmd += " -1"
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80 status = subprocess.call(cmd, shell=True)
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81 if status != 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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82 raise Exception("Problem with the execution of command!")
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83 toTar(options.outTarFileName, directory)
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84 shutil.rmtree(directory)
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